BLOGS

By now you’ve likely heard about the bacterium discovered in California’s Mono Lake:

The study, published in the journal Science, demonstrates that one of the most notorious poisons on Earth can also be the very stuff of life for some creatures.

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“Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus,” the researchers write in Science.

These six elements make up the nucleic acids — the A, C, T and G of DNA — as well as proteins and lipids. But there is no reason in theory why other elements should not be used. It is just that science never found anything alive that used them.

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.. it does suggest that astrobiologists looking for life on other planets do not need to look only for planets with the same balance of elements as Earth has.

“Our findings are a reminder that life-as-we-know-it could be much more flexible than we generally assume or can imagine,” said Wolfe-Simon.

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As cool as this is, arsenic is not a good substitute for phosphorus and so this is likely to be an isolated example. Part of the reason is basic chemistry; compared to the phosphate esters in DNA, arsenate esters are very unstable and are hydrolyzed remarkably fast. That makes this finding even more impressive, but it also precludes extensive substitution of arsenic for phosphorus in DNA-like genetic material.

The Harvard chemist Frank Westheimer wrote a memorable paper explaining “why nature chose phosphates” which can be found here. It explains based on basic principles of chemistry why phosphates rather than arsenates or silicates have been chosen by life. Must read for those who think alternative life-forms could be common.

So I would not call it “arsenic based DNA” just yet; the researchers themselves admit that they don’t know that the arsenic is replacing the phosphorus in DNA in exactly the right places.

You should reword your opening statement. They didn’t find bacteria with arsenic based DNA. They created bacteria with arsenic based DNA. What they found was a bacteria that lives in an arsenic rich environment and were able to make it change to arsenic based DNA by removing phosphorus from it’s environment.

Before reading this report above, I have only read about this indirectly from an online page linked in a friend’s Facebook post. Now I have only very briefly scanned through the Science article, so don’t claim to be an expert by any means. Still, I hope my comments might help others sort out different potential implications of this exciting discovery.

First, cool! This is great stuff and I am happy that the authors waited to publish their report in Science, rather than in a newspaper or online.

My first impression from reading an online blurb from my Facebook friend was that this was a fundamentally different lineage of life. Now that I have partly read the article, I am not so sure. First the authors claim that it is a bacterium, which to me would put it within one of the three known domains of life. That implies that the use of arsenic instead of phosphorus is a derived trait that is unique to this fascinating new lineage, but one would expect that it should still have retained plenty of historical baggage that would place it as a particular lineage within known bacterial diversity. It is important whether or not this microbe had ancestors with more conventional use of phosphorus for its genetic material and its equivalent of proteins. We definitely need to figure out how this microbe is related, if at all, to other known living organisms on Earth.

If this discovery is further confirmed (and science is quite good at revealing false claims), AND in the future it is possibly shown that this life form is outside the “clade” of previously known life, this discovery would assume entirely different significance. We already knew that all previously known life could be traced back to a single common microbial ancestor that was already quite a sophisticated life form, with cell membranes, DNA and RNA, plus the universally shared machinery to produce proteins on ribosomes, thousands of genes still found more than three billion years later in the genomes of contemporary living organisms. However, will the discovery of this new life form help us say anything new about life prior to the last common ancestor of all previously known life? The previous last universal common ancestor (was “LUCA” and could it become “PLUCA”?) has been as far as we could go back in time using the conventional methods of phylogenetic analysis, where we find that two lineages have more in common, due to shared ancestry, than a third lineage. We even were able to argue that two of the previously-known domains of life, Archaea and Eukarya, probably more recently shared a common ancestor than the third domain, Bacteria, although the history is also complicated by rather rampant swapping of genes. Ordinarily, phylogeneticist would not have been able to sort out the very deep relationships among these three known domains of life because there was no known outgroup for the LUCA clade. Outgroups are lineages outside of the clade of interest, and these are the primary way that a phylogeneticist can “root” a tree, in this case the tree of all previously known life. Fortunately, scientists have been able to figure out that some genes had already been duplicated pre-LUCA, so it proved feasible to use some gene trees to be effectively “rooted” with the inclusion of a related gene tree. This is a bit complicated but is essential for many interpretations about how cellular life forms have evolved.

To study the pre-LUCA origin of life, a fundamentally different approach was needed. This often involved coming up with a scenario for how pre-LUCA life might have gotten to that point of considerable sophistication, and then demonstrating (if possible) that the steps in such a progression are at least plausible. If the discovery of an arsenic-based life form is later found to be outside of the LUCA clade, then this might or might not help phylogeneticists push back the history of pre- or post-LUCA life. That would depend on whether the newly discovered life form was truly an independent lineage of life. It would not help at all if it were a completely independent life form. To me, it might be most interesting if was either a fourth domain of life, effectively inside the LUCA clade, or else is a more deeply diverging branch, indicating a deeper shared ancestor of all life on Earth. If it were revealed, instead, as a completely independent life form, this would of course be fascinating for different reasons.

Remembering the big splash “NASA” made about fossil “life forms” inside Martian rocks, I personally am going to remain skeptical. I am happy that NASA-funded astrobiologists are using the cost-effective approach of better exploring our own backyard. We still know very little about extreme environments right here on Earth and I do applaud NASA-funded astrobiologists for their efforts to explore these more thoroughly. I especially hope this discovery helps promote further exploration of deep sea habitats, where fundamentally different extreme environments are known to exist.

@6: On the contrary, one could argue it the other way (and I’m sure it will happen). What part of evolution would lead to DNA being able to change from phosphorus based to arsenic based? DNA seems to have a built in capability that would not give it an advantage in the natural world (on Earth at least).

I think the Intelligent Design folks will put this in the category of irreducible complexity. And it would seem to be a valid argument at this early stage…

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About Sheril Kirshenbaum

Sheril Kirshenbaum is a research scientist with the Webber Energy Group at the University of Texas at Austin's Center for International Energy and Environmental Policy where she works on projects to enhance public understanding of energy issues as they relate to food, oceans, and culture. She is involved in conservation initiatives across levels of government, working to improve communication between scientists, policymakers, and the public.
Sheril is the author of The Science of Kissing, which explores one of humanity's fondest pastimes. She also co-authored Unscientific America: How Scientific Illiteracy Threatens Our Future with Chris Mooney, chosen by Library Journal as one of the Best Sci-Tech Books of 2009 and named by President Obama's science advisor John Holdren as his top recommended read. Sheril contributes to popular publications including Newsweek, The Washington Post, Discover Magazine, and The Nation, frequently covering topics that bridge science and society from climate change to genetically modified foods. Her writing is featured in the anthology The Best American Science Writing 2010.
In 2006 Sheril served as a legislative Knauss science fellow on Capitol Hill with Senator Bill Nelson (D-FL) where she was involved in energy, climate, and ocean policy. She also has experience working on pop radio and her work has been published in Science, Fisheries Bulletin, Oecologia, and Issues in Science and Technology. In 2007, she helped to found Science Debate; an initiative encouraging candidates to debate science research and innovation issues on the campaign trail. Previously, Sheril was a research associate at Duke University's Nicholas School of the Environment and has served as a Fellow with the Center for Biodiversity and Conservation at the American Museum of Natural History and as a Howard Hughes Research Fellow. She has contributed reports to The Nature Conservancy and provided assistance on international protected area projects.
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Sheril is a graduate of Tufts University and holds two masters of science degrees in marine biology and marine policy from the University of Maine. She co-hosts The Intersection on Discover blogs with Chris Mooney and has contributed to DeSmogBlog, Talking Science, Wired Science and Seed. She was born in Suffern, New York and is also a musician. Sheril lives in Austin, Texas with her husband David Lowry.
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